I think the reason why you don’t see it there is the combination of the category mute and the topic mute.
Do you want to keep both? I think usually one of them is enough. Either you can have the topic level to be “normal” and the muted category hides the topic from topic lists, or you don’t mute the category but the individual topic in it you aren’t interested in.
I think a muted topic prevents notifications in cases like, for example, @mentions, while if only the category is muted you can still receive notifications about individual topics. That was a problem when the summaries were tested and used @mentions. But this has been changed for some time, so I think you no longer need a double mute.
But I agree that it should be possible to find muted topics in muted categories. Muted categories should not hide topics from this list created by the state=muted query string or the in:muted filter